Naturphilosophie attempts to comprehend nature in its totality and to outline its general theoretical structure, thus providing the foundational basis for the natural sciences. In developing their theories, the German Naturphilosophen found their inspiration in the natural philosophy of the Greek Ionian philosophers of antiquity. After its initial development by the German Idealist philosophers, many of the key insights of the Naturphilosophen have gone on to become a part of modern ontology and is now incorporated into the general philosophy of science.

As an approach to philosophy, Naturphilosophie was for most of the 19th and early 20th centuries misunderstood in the English-speaking countries because of early problems with translations and a lack of language skills among English-speaking philosophers. It quickly came under fire by English-speaking philosophers and over the years has been subjected to continuing criticism, though since the 1960s improved translations and better language skills among British and American scholars have led to a renewed interest and a better appreciation of the objectives of Naturphilosophie.

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The German Idealist philosopher Johann Gottlieb Fichte had attempted to show that the whole structure of reality follows necessarily from the fact of self-consciousness. He had arrived at a conception of the fundamental features of knowledge and of conduct as necessary elements in the attainment of self-consciousness. Fichte's idealism thus simultaneously rejected the conception of cognition and practice as reliant on the interaction of two real worlds, subject and object, and attempted to lay the foundation for all future philosophical systems. But, to Schelling, Fichte's doctrines appeared on the one hand to identify the ultimate ground of the universe of reason too closely with finite, individual Spirit, and on the other to threaten the reality of the world of nature by seeing it too much in the manner of subjective idealism, as a mere moment (albeit a necessary one) in the existence of the finite thinking mind. Fichte, it was seen, never managed, almost inevitably, to unite his system with the aesthetic view of nature to which Immanuel Kant's Critique of Judgment had pointed as an essential component in any complete philosophy.

Schelling took Fichte's position as his starting-point. From Fichte he derived the ideal of philosophy as fully unified and also the formal method to which he largely continued to adhere. In his earliest writings Schelling posited that nature should not be conceived as a merely abstract limit bounding the infinite striving of spirit, or as a mere series of necessary thoughts for mind. Nature must have reality for itself, a reality which does not stand in conflict with its ideal character, a reality whose inner structure is ideal and has its origin in spirit. Nature as the sum of what is objective, and intelligence as the complex of all the activities making up self-consciousness, appear thus as equally real, as equally exhibiting an ideal structure. We thus have the philosophy of nature and transcendental philosophy as the two complementary portions making up philosophy as a whole.

Inspired by this new conception Schelling hurriedly conceived his Naturphilosophie. Relying on Kant and a fragmentary knowledge of contemporary science, he produced in a short space of time the Ideen, the Weltseele, and the Erster Entwurf. Naturphilosophie has not fared well at the hands of modern science. Schelling, it is alleged, had neither the intellectual rigour nor the knowledge necessary to combine the abstract treatment of cosmological notions and concrete scientific investigation. His attempts at a construction of natural reality were weak, and gave rise to muddled and misguided speculation on matters of physics. At the same time there are original and sometimes valuable thoughts scattered through the writings on Naturphilosophie which remain of interest. As a criticism of scientific procedure, these writings retain a relevance despite their tendency to hasty and rash a priori and free-floating armchair theorizing about nature. Schelling characteristically wrote in his Freedom essay (1809): "It cannot be denied that it is a splendid invention to be able to designate entire points of view at once with such general epithets. If one has once discovered the right label for a system, everything else follows of its own accord and one is spared the trouble of investigating its essential characteristics in greater detail."

Schelling held that nature, since it has reality for itself, forms one completed whole. Its manifoldness does not destroy its fundamental unity. The divisions imposed on it by our ordinary perception and thought do not have absolute validity, but should be interpreted as the outcome of the single formative energy which is the soul or inner aspect of nature. We are able to apprehend and represent nature to ourselves in the successive forms which its development assumes since it is the same spirit of which we become aware in self-consciousness, though here unconsciously. The variety of its forms is not imposed on it externally, since there is no external teleology in nature. Nature is a self-forming whole, within which only natural explanations can be sought. The function of Naturphilosophie is to exhibit the ideal as springing from the real, not to deduce the real from the ideal. The continual change presented to us by experience, taken together with the thought of unity in productive force of nature, leads to the conception of the duality through which nature expresses itself in its varied products. The dynamic series of stages in nature, the forms in which the ideal structure of nature is realized, are matter, as the equilibrium of the fundamental expansive and contractive forces; light, with its subordinate processes (magnetism, electricity, and chemical action); organism, with its component phases of reproduction, irritability and sensibility.

Just as nature exhibits to us the series of dynamical stages of processes by which spirit struggles towards consciousness of itself, so the world of intelligence and practice exhibits the series of stages through which self-consciousness with its inevitable oppositions and reconciliations develops in its ideal form. The theoretical side of inner nature in its successive grades from sensation to the highest form of spirit, the abstracting reason which emphasizes the difference of subjective and objective, leaves an unsolved problem which is satisfied only in practical, individualizing activity. The practical, taken together with the theoretical, forces on the question of the reconciliation between the free conscious organization of thought and the apparently necessitated and unconscious mechanism of the objective world. In the notion of a teleological connection and in that which for spirit is its subjective expression, that is, art and genius, the subjective and objective find their point of union.

Nature and spirit, Naturphilosophie and Transzendentalphilosophie, are thus two in themselves complete but complementary parts of the whole. It was impossible for Schelling, whose thought was always striving for the reconciliation of differences, not to see nature and spirit as manifestations arising from an underlying unifying basis. However, he initially failed to find any characterization for this basis other than the merely negative one of indifference. The identity (or "absolute") which underlay all difference and relativity was to be characterized simply as neutrum (absolute undifferentiated self-equivalence).

At this juncture Schelling identified himself with Baruch de Spinoza, to whose thought he saw himself as approaching. The Darstellung meines Systems, and the expanded treatment in the lectures on a System der gesamten Philosophie und der Naturphilosophie insbesondere given in Würzburg in 1804, contain elements of Spinoza's philosophy.

Despite his efforts, it is doubtful if Schelling managed to establish a viable connection between his conceptions of nature and spirit and the primal self-identity of reason. In particular, it seems incredible that a solution could be offered by merely pointing to the absence of any distinguishing or differentiating feature. The absolute was left with no other function than that of removing all the differences which give form to thought. The criticisms of Fichte, and more particularly of Hegel (in the Preface to the Phenomenology of Spirit), point to the fatal defect in the conception of the absolute as mere featureless identity, notoriously ridiculed by Hegel as "the night in which all cows are black." Schelling, however, offered the counterargument that Hegel was merely lost in his head. To Schelling, the featureless Absolute was no mere concept arrived at by logical deduction, but a transcendental reality that could only be understood properly through direct experience, beyond logic and reason, such as through mystical contemplation (in religion) or aesthetic rapture (in art). In this respect, Schelling's philosophy bears some resemblance to the expositions of nondualism found, for example, in Zen Buddhism, Advaita Vedanta, and the theology of Meister Eckhart.

Vitalism - a Naturphilosophie-like idea in physiology. At the time of Naturphilosophie, it was heavily debated by physiologists and attacked by scientists such as Hermann von Helmholtz who wanted to reform physiology into a more mechanical and materialist science.